Variant report

Variant	rs11261469
Chromosome Location	chr8:86189699-86189700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10090196	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10091582	0.90[ASN][1000 genomes]
rs10099251	0.90[ASN][1000 genomes]
rs10106970	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10107686	0.84[ASN][1000 genomes]
rs10110461	0.89[ASN][1000 genomes]
rs10111971	0.90[ASN][1000 genomes]
rs1021583	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11261471	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12541299	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12541445	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12543256	0.96[ASN][1000 genomes]
rs12546106	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12550160	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12679400	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13259464	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1496533	0.86[ASN][1000 genomes]
rs1553016	0.90[ASN][1000 genomes]
rs1553017	0.89[ASN][1000 genomes]
rs16913681	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16913721	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17740658	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1809819	0.86[ASN][1000 genomes]
rs1845891	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1845892	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1908762	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2006767	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2132589	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2132590	0.98[ASN][1000 genomes]
rs2279700	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279701	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291786	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291787	0.84[ASN][1000 genomes]
rs2403083	0.82[ASN][1000 genomes]
rs2403084	0.82[ASN][1000 genomes]
rs2403085	0.83[ASN][1000 genomes]
rs2403086	0.83[ASN][1000 genomes]
rs28374336	0.90[ASN][1000 genomes]
rs28377260	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28439950	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564613	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28677919	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35558766	0.89[ASN][1000 genomes]
rs3779901	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4150893	0.81[ASN][1000 genomes]
rs4150897	0.81[ASN][1000 genomes]
rs4150944	0.81[ASN][1000 genomes]
rs4150962	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4150964	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4150974	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150977	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4609189	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4617148	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4739698	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4740045	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4740047	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6605610	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6605611	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6605613	0.89[ASN][1000 genomes]
rs6993316	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6994113	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7001359	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7004871	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7011001	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7821629	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7826511	0.82[ASN][1000 genomes]
rs7827175	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7829240	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7839129	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9329908	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024759	chr8:86162507-86361533	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539659	chr8:86162507-86361533	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv971674	chr8:86187966-86338484	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11261469	LRRCC1	cis	Esophagus Mucosa	GTEx
rs11261469	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs11261469	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs11261469	LRRCC1	cis	Artery Tibial	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86158400-86191400	Weak transcription	Pancreas	Pancrea
2	chr8:86158800-86191400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr8:86168000-86196200	Weak transcription	NHEK	skin
4	chr8:86168000-86199000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:86170600-86191800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr8:86170800-86204400	Weak transcription	Ovary	ovary
7	chr8:86172200-86191400	Weak transcription	Primary T cells from cord blood	blood
8	chr8:86174600-86198200	Weak transcription	Left Ventricle	heart
9	chr8:86175800-86191200	Weak transcription	Brain Hippocampus Middle	brain
10	chr8:86175800-86191800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr8:86176400-86195000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr8:86177600-86191200	Weak transcription	Right Ventricle	heart
13	chr8:86178000-86198200	Weak transcription	Aorta	Aorta
14	chr8:86178200-86193400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr8:86179000-86191200	Weak transcription	Stomach Mucosa	stomach
16	chr8:86181200-86191400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:86181600-86190800	Weak transcription	Small Intestine	intestine
18	chr8:86181600-86191400	Weak transcription	Fetal Lung	lung
19	chr8:86182600-86196000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr8:86183000-86190000	Weak transcription	Colonic Mucosa	Colon
21	chr8:86183800-86190200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr8:86183800-86190800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:86184000-86190400	Strong transcription	Fetal Intestine Small	intestine
24	chr8:86184200-86190200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr8:86184400-86191200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr8:86185400-86190000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:86185600-86190200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:86185600-86190200	Weak transcription	HepG2	liver
29	chr8:86186200-86191400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr8:86186400-86190800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr8:86186400-86191400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:86186600-86198800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr8:86187200-86189800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr8:86187400-86190000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr8:86187800-86190400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr8:86187800-86195400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr8:86188200-86190000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:86188200-86190000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr8:86188200-86190200	Strong transcription	Gastric	stomach
40	chr8:86188200-86190200	Strong transcription	Lung	lung
41	chr8:86188600-86190200	Strong transcription	Fetal Stomach	stomach
42	chr8:86188800-86191400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr8:86188800-86191400	Weak transcription	Esophagus	oesophagus
44	chr8:86188800-86194400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr8:86189200-86190200	Strong transcription	Liver	Liver
46	chr8:86189200-86190200	Strong transcription	Fetal Intestine Large	intestine
47	chr8:86189400-86189800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr8:86189400-86190000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr8:86189600-86190000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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